The ancient Christian community of Syria is caught in the crossfire of a civil war, causing many to flee to neighbouring countries. They leave behind them a nation whose strife will have a profound impact on the complexities of the entire Middle East

The moment she saw the rosary on my bed, the chambermaid of my hotel in Aleppo smiled ecstatically. She was an Eastern (Greek) Orthodox who could claim to trace her roots back to the time of St Paul. Christianity flourished as long in Syria as it did in Iraq and thrived particularly well during the Alawite rule of the Assads since Hafez Assad's Baathist coup in 1970.

But now Christians make up only 10 per cent of the population of Syria, and they are haemorrhaging from the region under the pressure of militant Islam. The peaceful protests that first began 16 months ago as Syrians demanded regime change have been overtaken by the spread of jihadist groups following President Bashar al-Assad's violent clamp down against peaceful protests.

The mantra "Islam is the solution", on the lips of so many in the region today, has exacerbated the flight of Christians.

Despite heroic stories of the protection given by members of Syria's Sunni majority to Christian shopkeepers, Christian refugees are fleeing into northern Lebanon as fast as Iraq's three million refugees are pouring from Syria back into Iraq. Indeed, one of the reasons that Russia has refused to abandon President Assad is its feeling of responsibility for Syria's Orthodox Christian community.

Meanwhile some 90 per cent of the Christians of Homs are said to have fled to Jordan recently, persecuted by a group claiming to belong to Al Qaeda. And among the four members of President Assad's inner circle killed by the Free Syrian Army on 17 July was General Daoud Rajiha, Syria's Eastern Orthodox defence minister. The papal nuncio, Archbishop Mario Zenari, described the conflict as "dragging the country towards, destruction, towards unspeakable suffering and death". Some of the rebels today angrily accuse Syria's Christians of collaborating with the regime but a fair number of Christians have supported the rebellion which began as a mere protest movement against a still popular President Assad in March 2011.

It is a far cry from his taking of power 12 years ago. When his strongman father died in 2000, many Syrians feared civil war but the young Bashar, an ophthalmologist from London, married to a pretty, bright, Acton-born girl of Syrian origin, offered his father's many enemies an olive branch and gave reformist speeches. He had not been groomed for power but filled the void as heir when his favoured elder brother, Basil, was killed in a car crash. Unfortunately, his attempts at reform were blocked by Syria's myriad security forces who continued to carry out violent operations, not least the alleged assassination of Lebanon's popular President Rafik Hariri in 2005.

Although human rights in Syria remained poor, with opponents of the regime tortured and sometimes killed, I found the atmosphere in the streets much more liberal than during much of the 1980s when memories of the 1982 slaughter of Islamist prisoners in their cells and the massacre of the people of Hama were still fresh. Nobody followed me, as once would have been the case. Wherever I wandered in the lanes of Damascus' lovely old Bab Tuma district, I was invited for sherbet drinks, dinner and games of chess. Children ran out of their courtyards to show me their homework. It was obvious, too, that the middle classes supported a regime which they reckoned ensured stability. The ruling Alawites, 13 per cent of the population, saw other minorities, Syrian Christians, Armenians, Druze and Kurds, as unthreatening allies.

Then last year everything began to change. To its cost the regime had not allowed an Arab Spring to emerge. There was to be no Tahrir Square in Damascus. This might have relieved the pressure by giving the people a voice. However, the Assad dynasty and the Alawites, who fill top positions in the Government and the army, feel extremely vulnerable. It is probable that Bashar had not had the courage to withstand his father's security men, represented on the streets today by the regime's thugs, the Shabiha ("ghosts" in Arabic). Last week the rebels executed members of the notorious Berri family who had become Shabiha killers. The death toll on both sides has now reached 20,000.

Assad claimed, just as Saddam in Iraq, Ben Ali in Tunisia and Mubarak in Egypt had done, that the alternative to his rule was a Jihadi Salafi movement which would impose Sharia law and suppress social freedoms. Hard-line Muslims, some from Britain, have, indeed, joined the rebels and some correspondents point out that the US may be supporting the very Islamist elements in Syria that it is fighting in Afghanistan. President Obama has given the go-ahead to help finance the rebels but US support remains cautious with an election approaching. Al Qaeda's amanuensis, Ayman al-Zawahiri, has been quoted as saying that he recognises an opportunity for Syria to become the new incubator for militant, Salafist Islam. The rebels have at times been as cruel as the army. At Jisr al Shughur in April last year they are said to have massacred 100 soldiers. Nevertheless, the militant Islamist element remains limited for the moment.

Like Saddam Hussein's Iraq, Assad's Syria is, or was, a country steered by its minorities. Historically persecuted by the Sunni majority, the Alawites (said to be disciples of the Prophet Muhammad's nephew and son-in-law Ali), an esoteric sub-sect of Shiism, fought the French after the First World War but were then championed by France as proxy rulers. However, some Sunni imams dismiss the Alawites not as Shia Muslims but as heretics, even pagans, and mistrust their alliance with Syria's other minorities.

Reasonable Muslims claim that Sunni-Shia hatred is largely a Western invention, although now becoming a self-fulfilling prophecy. Both sects have always performed the Hajj to Mecca together, for example. The Ayatollah Khomeini downplayed Iran's Shia identity, appealing to a pan-Islamic Weltanschauung. That has since changed. Today Iran supports Syria as well as their mutual clients, the Shia Hezbollah in Lebanon and the Sunni Hamas movement in Gaza. By contrast, Saudi Arabia and Qatar, and latterly Turkey, support the Sunni rebels. The Al Jazeera television channel funded by Qatar and the Al Arabiya channel by Saudi Arabia both give voice to the rebels. Saudi Arabia, committed to its fundamentalist and localised Wahhabi philosophy, is uncomfortable with the impoverished Shia minority living in its oil-rich Hasa province. Had Saddam Hussein been allowed to keep Kuwait in 1990 he might have gone on to absorb Hasa, thereby creating the notorious and oil-rich "Shia Arc" which Sunni nations fear.

During the 1990 Gulf War, Syria supported the US and Britain and relations blossomed. Despite its war footing over the Golan Heights, occupied by Israel in the 1967 war, Syria was no longer deemed a terrorist state.

However, Assad's ferocious response to the protest movement meant that the West could no longer be seen to be supporting his regime. Meanwhile, Syria's neighbours had their own reasons for supporting the rebels. Turkey wants to please Europe during its endless quest for EU membership. Recep Tayyib Erdogan's moderate Islamic AK Party would also welcome a moderate Islamic regime in Syria similar to its own. In Egypt, the Muslim Brotherhood, the beating heart of Islamism throughout the world, has an Islamist majority in parliament and a moderate Islamist President in Mohammed Mursi. So post-Mubarak Egypt, too, would favour a regime similar to its own.

The fall of the Alawites will weaken the Shia in Lebanon who now make up about 60 per cent of the population as well as Hezbollah, which is popular for having successfully resisted two Israeli invasions. This must be the main reason for Israel welcoming Assad's now inevitable downfall. Syria had used tough words against Israel for local consumption but taken virtually no action against the Jewish state and was in fact a compliant neighbour. If an Islamist regime emerges it will take a harder line against Israel.

Iran will be the biggest loser. Saeed Jalili, Iran's chief negotiator, is due to meet Hassan Nasrallah, the Hezbollah leader, in Beirut this week to prepare for its response to the dramatic changes that are to come. Israel, which bombed a supposed nuclear site in Syria in 2007, still has Iran's nuclear facilities in its sights. The big changes afoot in Syria are going to alter the make-up of the region dramatically. Although they trouble Iran, they may not favour the interests of the US, Europe or Israel, either. Kofi Annan's resignation last week as international envoy to Syria suggests that reconciliation is no longer possible.